Contacts of the strand formed by residues 51 - 54 (chain O) in PDB entry 2BDI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TRP 51 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46O LEU* 3.4 2.8 - - - +
47O VAL* 3.2 20.1 + - + -
48O HIS* 3.2 41.0 + + + +
50O GLN* 1.3 85.5 + - + +
52O VAL* 1.3 62.3 + - - +
53O LEU 4.2 0.4 - - - -
87O LEU* 5.0 4.3 - - + -
89O VAL* 5.0 8.5 - - + -
105O LEU* 3.9 27.8 - - + -
106O ILE 3.4 8.3 - - - -
107O LYS* 3.3 66.0 - - + +
108O LEU* 3.6 1.4 - - - +
241O THR* 3.9 19.5 - - + -
242O VAL* 3.1 60.4 + - + +
244O ALA* 6.1 0.4 - - - -
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Residues in contact with VAL 52 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O ALA* 4.2 17.5 - - + -
33O LEU* 5.0 3.1 - - + -
44O GLY* 3.9 14.8 - - - -
45O VAL 3.5 4.9 - - - +
46O LEU* 3.9 17.9 - - + -
51O TRP* 1.3 75.0 - - - +
53O LEU* 1.4 70.7 + - - +
54O SER* 4.8 0.4 - - - -
65O ILE* 4.2 21.8 - - + -
67O LEU* 5.1 2.0 - - + -
104O MET 3.8 0.7 - - - +
105O LEU* 3.6 3.5 - - - -
106O ILE* 2.8 60.0 + - + +
108O LEU* 4.2 9.6 - - + -
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Residues in contact with LEU 53 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44O GLY* 3.0 6.4 - - - -
45O VAL* 2.6 47.7 + - + +
47O VAL* 3.7 17.9 - - + +
52O VAL* 1.4 68.8 - - - +
54O SER* 1.3 72.2 + - - +
103O LEU* 4.6 10.3 - - + -
104O MET 3.5 16.6 - - - +
105O LEU* 3.6 18.2 - - + -
123O ILE* 3.9 25.8 - - + -
209O LEU* 4.0 8.7 - - + -
212O LEU* 4.0 13.0 - - + +
231O LEU* 3.8 25.1 - - + -
238O ILE* 4.2 6.1 - - + -
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Residues in contact with SER 54 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O LEU* 4.2 4.3 - - - +
43O SER 2.9 22.2 + - - -
44O GLY* 4.1 2.0 - - - -
52O VAL* 4.8 0.9 - - - -
53O LEU* 1.3 79.3 - - - +
55O ALA* 1.3 67.6 + - - +
58O CYS* 4.2 9.0 - - - +
103O LEU* 3.3 5.2 - - - -
104O MET* 2.7 53.8 + - - -
106O ILE* 4.8 9.4 - - - -
196O GLY* 4.0 2.3 - - - -
212O LEU* 3.5 17.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il